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The influence of disease categories on gene candidate predictions from model organism phenotypes

Anika Oellrich, Sebastian Koehler, Nicole Washington, Chris Mungall, Suzanna Lewis, Melissa Haendel, Peter N Robinson, Damian Smedley
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Future work on computational disease gene prediction using phenotype data would benefit from methods that take into account the disease category and the source of model organism data.  ...  Conclusions: In conclusion, our automated disease gene candidate predictions are highly dependent on the organism used for the predictions and the disease category being studied.  ...  Acknowledgements This work was supported by core infrastructure funding from the Wellcome Trust and National Institutes of Health  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-s1-s4">doi:10.1186/2041-1480-5-s1-s4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25093073">pmid:25093073</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4108905/">pmcid:PMC4108905</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xf6e7ytware2lebwv4ptnoc25y">fatcat:xf6e7ytware2lebwv4ptnoc25y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20140714082107/http://www.jbiomedsem.com/content/pdf/2041-1480-5-S1-S4.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b3/ef/b3efdb1bdbb8e517eda064a3fda43eb04795d376.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-s1-s4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108905" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Analysis of the human diseasome using phenotype similarity between common, genetic and infectious diseases

Robert Hoehndorf, Paul N. Schofield, Georgios V. Gkoutos
<span title="2015-06-08">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Phenotypes are the observable characteristics of an organism arising from its response to the environment.  ...  Phenotypes associated with engineered and natural genetic variation are widely recorded using phenotype ontologies in model organisms, as are signs and symptoms of human Mendelian diseases in databases  ...  The disease network was visualized using the Gephi graph visualization tool 47 , and the disease network browser was generated with Gephi's Sigma-js export plugin (http://blogs.oii.ox.ac.uk/vis/).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep10888">doi:10.1038/srep10888</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26051359">pmid:26051359</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4458913/">pmcid:PMC4458913</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7to4snmfk5b7hee3gyfmg6t63i">fatcat:7to4snmfk5b7hee3gyfmg6t63i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809124721/http://repository.kaust.edu.sa/kaust/bitstream/10754/556899/1/srep10888.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/d9/71d9ba2dcf11ddbabfe54776eae9f3e00a164317.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/srep10888"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458913" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Drosophilaand genome-wide association studies: a review and resource for the functional dissection of human complex traits

Michael F. Wangler, Yanhui Hu, Joshua M. Shulman
<span title="2017-02-01">2017</span> <i title="The Company of Biologists"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s6p4bs5qazhcbhqumqmuipbqh4" style="color: black;">Disease Models &amp; Mechanisms</a> </i> &nbsp;
investigations of the implicated genes will powerfully inform our understanding of human disease.  ...  Although the susceptibility variants identified by GWAS usually have only modest effects on individual disease risk, they contribute to a substantial burden of trait variation in the overall population  ...  Acknowledgements The authors are grateful to Juan Botas and Neil Hanchard for feedback on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1242/dmm.027680">doi:10.1242/dmm.027680</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28151408">pmid:28151408</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5312009/">pmcid:PMC5312009</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cbavqvotxrcvrckxlvzdbmhogy">fatcat:cbavqvotxrcvrckxlvzdbmhogy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720211628/http://dmm.biologists.org/content/dmm/10/2/77.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e1/65/e165a17bb1f5586851aa5065b32ea75440d33f6a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1242/dmm.027680"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312009" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

Larisa N Soldatova, Philippe Rocca-Serra, Michel Dumontier, Nigam H Shah
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
, representation of scientific results and gene candidate prediction.  ...  The six papers selected for this supplement span a wide range of topics including: ontology-based data integration, ontology-based annotation of scientific literature, ontology and data model development  ...  We are grateful for help from Sarah Headley from BioMed Central in putting this supplement together.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-s1-i1">doi:10.1186/2041-1480-5-s1-i1</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4108850/">pmcid:PMC4108850</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cyqs6udi2nbqfio3cj34qg7eq4">fatcat:cyqs6udi2nbqfio3cj34qg7eq4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4108850/PMC4108850-2041-1480-5-S1-I1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/35/2f/352fb240b9965b45ba98d35144b6d00563f354f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-5-s1-i1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108850" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Causality in Genetics: The Gradient of Genetic Effects and Back to Koch's Postulates of Causality

A. J. Marian
<span title="2014-01-16">2014</span> <i title="Ovid Technologies (Wolters Kluwer Health)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zo5fftfyifagxbgtfyochmz3im" style="color: black;">Circulation Research</a> </i> &nbsp;
Marian Center for Cardiovascular Genetics, Institute of Molecular Medicine and Department of Medicine University of Texas Health Sciences Center at Houston Texas Heart Institute Houston, TX  ...  Model organisms can be valuable in supporting the causal role of candidate variants if the introduction of candidate variants into the model organism could result in a phenotype that resembles the intended  ...  must be supported by the mechanistic data, such as induction of the intended phenotype in a model organism on introduction of the variant and reversal of the phenotype on its removal or shutting down  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/circresaha.114.302904">doi:10.1161/circresaha.114.302904</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24436434">pmid:24436434</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3896867/">pmcid:PMC3896867</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cwcj3agqfnfgdcso272vozdue4">fatcat:cwcj3agqfnfgdcso272vozdue4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219192712/http://pdfs.semanticscholar.org/1a44/be3eba71d3af89afd3b401d75dd553f79086.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1a/44/1a44be3eba71d3af89afd3b401d75dd553f79086.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1161/circresaha.114.302904"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896867" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mendelian gene identification through mouse embryo viability screening [article]

Pilar Cacheiro, Carl Henrik Westerberg, Jesse Mager, Mary E. Dickinson, Lauryl M.J. Nutter, Violeta Mu&ntildeoz-Fuentes, Chih-Wei Hsu, Ignatia B. Van den Veyver, Ann M. Flenniken, Colin McKerlie, Stephen A. Murray, Lydia Teboul (+21 others)
<span title="2022-01-07">2022</span> <i title="Cold Spring Harbor Laboratory"> medRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Finally, we investigated unsolved cases from the 100,000 Genomes Project recruited under this disease category to look for signs of enrichment of biallelic predicted pathogenic variants among early gestation  ...  lethal genes and highlight two novel candidates with phenotypic overlap between the patients and the mouse knockout.  ...  It also highlights the power of cross-species phenotype analysis by integrating model organism resources with data from large scale sequencing programs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.01.07.22268899">doi:10.1101/2022.01.07.22268899</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4yje2en2hjd6plqo452n4inibq">fatcat:4yje2en2hjd6plqo452n4inibq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220112141359/https://www.medrxiv.org/content/medrxiv/early/2022/01/07/2022.01.07.22268899.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e7/22/e7223f86d6bded4fcfed059183e785b6201b8119.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2022.01.07.22268899"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> medrxiv.org </button> </a>

Phenotypes of Patients with "Simple" Mendelian Disorders Are Complex Traits: Thresholds, Modifiers, and Systems Dynamics

Katrina M. Dipple, Edward R.B. McCabe
<span title="">2000</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ho5llzhlhzhmrlusxzz4j2bery" style="color: black;">American Journal of Human Genetics</a> </i> &nbsp;
Elizabeth Neufeld (UCLA), for suggesting that we consider polymorphic influences on flux to explain genotype-phenotype discordance.  ...  The research that led to the formulation of these models was supported, in part, by National Institute of Child Health and Human Development grant R01 HD22563.  ...  A study of patients from seven European centers evaluated a model for prediction of four phenotypic categories on the basis of PAH genotype (Guldberg et al. 1998 ).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1086/302938">doi:10.1086/302938</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10793008">pmid:10793008</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1378056/">pmcid:PMC1378056</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okwjoy36bnhxhaccvbamcvnop4">fatcat:okwjoy36bnhxhaccvbamcvnop4</a> </span>
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An Automated Functional Annotation Pipeline That Rapidly Prioritizes Clinically Relevant Genes for Autism Spectrum Disorder

Olivia J. Veatch, Merlin G. Butler, Sarah H. Elsea, Beth A. Malow, James S. Sutcliffe, Jason H. Moore
<span title="2020-11-27">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Of the 956 ASD-implicated genes in the full set, 18 were flagged based on evidence in all categories.  ...  Fewer genes from randomly drawn sets were annotated in all categories (x = 8.02, sd = 2.56, p = 7.75 × 10−4).  ...  Ultimately, 18 ASD candidate genes were prioritized based on annotation in each step of the pipeline, which was more than the average number of genes from random gene sets (X 2 = 11.30, p = 7.75 × 10 −  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21239029">doi:10.3390/ijms21239029</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33261099">pmid:33261099</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jn6d5rgjhrckxcmjnvrvhftzai">fatcat:jn6d5rgjhrckxcmjnvrvhftzai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201129232954/https://res.mdpi.com/d_attachment/ijms/ijms-21-09029/article_deploy/ijms-21-09029.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/bd/e5bdc0a3ce4a50cea42b4c7723906d044bdd4762.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21239029"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

A Systems Approach Identifies Networks and Genes Linking Sleep and Stress: Implications for Neuropsychiatric Disorders

Peng Jiang, Joseph R. Scarpa, Karrie Fitzpatrick, Bojan Losic, Vance D. Gao, Ke Hao, Keith C. Summa, He S. Yang, Bin Zhang, Ravi Allada, Martha H. Vitaterna, Fred W. Turek (+1 others)
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5ihveavyobfs3mlzee7cjt7mfe" style="color: black;">Cell Reports</a> </i> &nbsp;
Graphical Abstract Highlights d A large, multiscale dataset to model interactions between stress and sleep in mice d Reveals a dynamic genetic landscape and striatal gene networks for stress and sleep  ...  ACCESSION NUMBERS Raw and processed RNA-Seq gene expression data are available via the Gene Expression Omnibus database (accession number GEO:GSE60312).  ...  Circles and squares are colored according to phenotype categories, with colors assigned to genes from the category of the phenotypes for which the genes test causal.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2015.04.003">doi:10.1016/j.celrep.2015.04.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25921536">pmid:25921536</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4797932/">pmcid:PMC4797932</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z5lhaecwqvbp5n7gh6q76tazeu">fatcat:z5lhaecwqvbp5n7gh6q76tazeu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170924032220/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/0ce/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMjIxMTEyNDcxNTAwMzc4Mg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f7/ed/f7ed2654c1fdb088ecc256b4e32dd8200ded3af2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.celrep.2015.04.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4797932" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Network-based global inference of human disease genes

Xuebing Wu, Rui Jiang, Michael Q Zhang, Shao Li
<span title="2008-05-06">2008</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oayrvwhnr5a2jm4pbva2dvz3ui" style="color: black;">Molecular Systems Biology</a> </i> &nbsp;
The predicted genetic landscape of over 1000 human phenotypes, which reveals the global modular organization of phenotypegenotype relationships.  ...  On the basis of the assumption that phenotypically similar diseases are caused by functionally related genes, we propose a computational framework that integrates human protein-protein interactions, disease  ...  Acknowledgements We thank Dr HG Brunner and his laboratory for the generosity of providing us with the phenotype network data, and Dr Xuegong Zhang, Dr Yuanlie Lin and members in our laboratory for useful  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/msb.2008.27">doi:10.1038/msb.2008.27</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18463613">pmid:18463613</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2424293/">pmcid:PMC2424293</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ibdizmjvpbdodhakmlfgh3ovqe">fatcat:ibdizmjvpbdodhakmlfgh3ovqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813045907/http://msb.embopress.org/content/msb/4/1/189.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d7/9f/d79feadfd8f3de6d51913ee95221bd35142a23d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/msb.2008.27"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2424293" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Recent Advances in Network-based Methods for Disease Gene Prediction [article]

Sezin Kircali Ata, Min Wu, Yuan Fang, Le Ou-Yang, Chee Keong Kwoh, Xiao-Li Li
<span title="2020-07-19">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Since molecular networks are able to capture complex interplay among molecules in diseases, they become one of the most extensively used data for disease-gene association prediction.  ...  In this survey, we aim to provide a comprehensive and an up-to-date review of network-based methods for disease gene prediction. We also conduct an empirical analysis on 14 state-of-the-art methods.  ...  In this survey, we aim to conduct an empirical analysis on disease gene prediction task using different methods from the above three categories.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.10848v1">arXiv:2007.10848v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhrspbsj6zfpfhwa42mzjp4lvy">fatcat:zhrspbsj6zfpfhwa42mzjp4lvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200723201229/https://arxiv.org/pdf/2007.10848v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/41/da/41da11e78994d1dc4feaf09b3bc46b1f05cdf228.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2007.10848v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation

Hong Dang, Deepika Polineni, Rhonda G. Pace, Jaclyn R. Stonebraker, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Lisa J. Strug, Wanda K. O'Neal, Michael R. Knowles, Dylan Glubb
<span title="2020-11-30">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
The results help to prioritize genes in the GWAS regions, predict direction of gene expression regulation, and identify new candidate modifiers throughout the genome for potential therapeutic development  ...  HLA Class II genes on chr6, and CEP72, EXOC3, and TPPP near the GWAS peak on chr5 are most consistently associated with CF lung disease severity across the tissues tested.  ...  Manichaikul, University of Virginia, Center for Public Health Genomics, for guidance, advisement, and discussion. We also like to thank Dr. Hae Kyung Im and lab, University of Chicago,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0239189">doi:10.1371/journal.pone.0239189</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33253230">pmid:33253230</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/acyhtl5oazaelg5s75qnqqw62q">fatcat:acyhtl5oazaelg5s75qnqqw62q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201203190303/https://journals.plos.org/plosone/article/file?id=10.1371%2Fjournal.pone.0239189&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/37/62374cc6792050f8240872fe485af0f453634e17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0239189"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Cancer Gene Prediction Using a Network Approach [chapter]

Xuebing Wu, Shao Li
<span title="2010-05-04">2010</span> <i title="CRC Press"> Cancer Systems Biology </i> &nbsp;
One limitation of this approach is that the SVM requires at least 10 known disease-related genes to train the model and to predict novel disease genes.  ...  We choose to directly model the correlation between disease phenotypic similarity and gene functional relatedness, and use the correlation to prioritize candidate genes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/9781439811863-c11">doi:10.1201/9781439811863-c11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jzyeajibx5gnbg5dskqedx6nwm">fatcat:jzyeajibx5gnbg5dskqedx6nwm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150513110953/http://bioinfo.au.tsinghua.edu.cn:80/member/lishao/Paper-SLi/10CSB%20Chap11.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/39/b1/39b1b0407bfb06fdf991d4f274b5405a7c469264.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1201/9781439811863-c11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Computational Approaches for Disease Gene Identification [article]

Peng Yang
<span title="2017-05-21">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The performance of Disease gene prediction models are limited by potential bias of single learning models and incompleteness and noise of single biological data sources, therefore ensemble learning models  ...  Recent approaches have applied the concept of 'guilty by association' to investigate the association between a disease phenotype and its causative genes, which means that candidate genes with similar characteristics  ...  Major Contributions and Organization As mentioned earlier, the ultimate goal of this research is to prioritize candidate disease genes from hundreds of candidate genes on the whole genome.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1704.03548v2">arXiv:1704.03548v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/obp2u37rovcsxenz4trbojz3qu">fatcat:obp2u37rovcsxenz4trbojz3qu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201001061555/https://arxiv.org/ftp/arxiv/papers/1704/1704.03548.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/53/49/5349ff16a6c564a1947129f0fe4d820a69f65953.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1704.03548v2" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Prediction of gene–phenotype associations in humans, mice, and plants using phenologs

John O Woods, Ulf Singh-Blom, Jon M Laurent, Kriston L McGary, Edward M Marcotte
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: In this work, we develop an unsupervised algorithm for ranking phenolog-based candidate disease genes through the integration of predictions from the k nearest neighbor phenologs, comparing classifiers  ...  Such "orthologous phenotypes," or "phenologs," are examples of deep homology, and may be used to predict additional candidate disease genes.  ...  Figure 1 1 Prediction of disease-genes from orthologous phenotypes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-203">doi:10.1186/1471-2105-14-203</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23800157">pmid:23800157</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3704650/">pmcid:PMC3704650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t4xqublrurgltfqh64t2dhiypu">fatcat:t4xqublrurgltfqh64t2dhiypu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830062230/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-14-203?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/70/19/7019328913ebd45ba4551bec1c057feeaeb0d583.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-203"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3704650" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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